Climberben,
The answer is the always popular "what do you want out of your GT/CS. If you want it to retain its value and rarity, you need to keep it original. Now if you want a car with more power and top end speed, then go with the engine swap. Either way, KEEP the original engine. Remember, once you change an antique, which is now a restomod, it is now something you like, but the down side is that it does not appeal to the true antique mustang owner. So if you do not plan on selling it any time soon, then go ahead and make the change.
Doug